Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005496.1 Kokia drynarioides strain JFW-HI SEQ_119559, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 26356
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:841 original size:2 final size:2
Alignment explanation
Indices: 834--865 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
824 TATTTCTTTA
834 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
866 TGTAGGGCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3870 original size:14 final size:14
Alignment explanation
Indices: 3851--3881 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3841 TTTGAATTAT
3851 AATGCCACTAATCC
1 AATGCCACTAATCC
*
3865 AATGCCGCTAATCC
1 AATGCCACTAATCC
3879 AAT
1 AAT
3882 AGTTTAGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.32, G:0.10, T:0.23
Consensus pattern (14 bp):
AATGCCACTAATCC
Found at i:7399 original size:12 final size:12
Alignment explanation
Indices: 7373--7432 Score: 52
Period size: 12 Copynumber: 4.9 Consensus size: 12
7363 ATAACAAACA
*
7373 TTTTCTTCT-TC
1 TTTTCTTTTCTC
7384 TTTTCTTTTCTC
1 TTTTCTTTTCTC
* *
7396 TTTTATTTTTTC
1 TTTTCTTTTCTC
7408 -TTTCTTTTTCTC
1 TTTTC-TTTTCTC
7420 ATTTTCCTTTTCT
1 -TTTT-CTTTTCT
7433 AAGTGACTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
11 11 0.28
12 18 0.46
14 9 0.23
15 1 0.03
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTCTTTTCTC
Found at i:7430 original size:31 final size:30
Alignment explanation
Indices: 7373--7430 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
7363 ATAACAAACA
7373 TTTTCTTCTTCTTTTCTTTTCTCTTTTATT
1 TTTTCTTCTTCTTTTCTTTTCTCTTTTATT
7403 TTTTCTTTCTT-TTTCTCATTTTC-CTTTT
1 TTTTC-TTCTTCTTT-TC-TTTTCTCTTTT
7431 CTAAGTGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
30 8 0.32
31 12 0.48
32 5 0.20
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (30 bp):
TTTTCTTCTTCTTTTCTTTTCTCTTTTATT
Found at i:10337 original size:20 final size:21
Alignment explanation
Indices: 10312--10350 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
10302 GCAAGGAATT
10312 TGAAAC-AACAAAAGTAAAAG
1 TGAAACAAACAAAAGTAAAAG
*
10332 TGAAACAAATAAAAGTAAA
1 TGAAACAAACAAAAGTAAA
10351 TAACAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.67, C:0.08, G:0.13, T:0.13
Consensus pattern (21 bp):
TGAAACAAACAAAAGTAAAAG
Found at i:17696 original size:30 final size:30
Alignment explanation
Indices: 17662--17734 Score: 146
Period size: 30 Copynumber: 2.4 Consensus size: 30
17652 AGATTCGGTT
17662 TCTTGATTTTCTTGAAAACAAGAAAGTGAA
1 TCTTGATTTTCTTGAAAACAAGAAAGTGAA
17692 TCTTGATTTTCTTGAAAACAAGAAAGTGAA
1 TCTTGATTTTCTTGAAAACAAGAAAGTGAA
17722 TCTTGATTTTCTT
1 TCTTGATTTTCTT
17735 TTTTGGTCGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (30 bp):
TCTTGATTTTCTTGAAAACAAGAAAGTGAA
Found at i:18113 original size:12 final size:12
Alignment explanation
Indices: 18091--18134 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
18081 TGTATGGGCA
18091 TCTTCTTCTTTT
1 TCTTCTTCTTTT
18103 TCATT-TTCTTTT
1 TC-TTCTTCTTTT
18115 TCTTCTTCTTTT
1 TCTTCTTCTTTT
*
18127 TCCTCTTC
1 TCTTCTTC
18135 AGAACTCTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 2 0.07
12 25 0.86
13 2 0.07
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.70
Consensus pattern (12 bp):
TCTTCTTCTTTT
Found at i:19742 original size:9 final size:8
Alignment explanation
Indices: 19728--19768 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
19718 CCACAGAATA
19728 TTTTTTTC
1 TTTTTTTC
19736 TTTTTTTC
1 TTTTTTTC
*
19744 TTTTTCTC
1 TTTTTTTC
* *
19752 GTATTTTC
1 TTTTTTTC
19760 TTTTTTTC
1 TTTTTTTC
19768 T
1 T
19769 CGACTTTTTG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.80
Consensus pattern (8 bp):
TTTTTTTC
Done.